Youth with inflammatory bowel disease (IBD) demonstrate deficits in lean mass (LM) placing them at increased risk for future health problems, including reduction of bone mass and impaired bone architecture. Research suggests that deficits in LM are multifactorial, including influences from the disease and its treatment, and health behaviors such as diet and physical activity. Based on a systematic literature review examining factors related to LM deficits in IBD, this article presents a conceptual model to explain the development of LM in youth with IBD. The model considers predictors of LM across 4 domains: demographic; medical; diet; and physical activity. Much existing research is cross-sectional, but suggests multiple factors work together to promote or inhibit LM accrual in youth with IBD. The conceptual model, developed based on empirical findings to date, can be used to understand and further elucidate the process through which LM is developed and maintained, to inform the development of empirically supported clinical interventions, and to guide future research objectives and priorities.